ABI Prism® 7900HT Sequence Detection System ... - OpenWetWare

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Basic Software Skills Tutorial About This Tutorial This tutorial will: ♦ Teach you to create, save, print, export, and import SDS plate documents ♦ Familiarize you with the basic components of the SDS software interface ♦ Explain how to customize and arrange the user interface to suit your needs ♦ Teach you to use the hand-held bar code reader ♦ Provide you with time-saving devices to increase your effectiveness on the SDS software Lesson 1: Using Plate Documents Using the Online Version of the Basic Skills Tutorial The SDS Online Help features a version of this tutorial. If you prefer to follow the online tutorial open the SDS Online Help as follows: Step Action 1 If not already active, launch the SDS software as explained on page 3-7. The SDS software workspace appears. 2 From the Help menu, select SDS Online Help. 3 When the SDS Online Help appears, select Basic Skills Tutorial from the list of options. 4 Follow the directions displayed on your screen. EveryplaterunontheABIPRISM 7900HT Sequence Detection System requires the creation of a plate document within the SDS software. A plate document is a virtual representation of a consumable used to contain samples and reagents during a sequence detection run. The software uses the plate document to coordinate the operation of the instrument (thermal cycling and data collection), to organize and store the data gathered during the PCR, and to analyze the run data. The SDS software can produce the two types of plate document files described in the table below. Plate Document File Extension Description ABI PRISM SDS Single Plate ABI PRISM SDS Template Document *.sds SDS Single Plate Documents are the primary file you will use. They are generated for every kind of experiment and are generally used to run plates. *.sdt Although optional, templates are useful as time-saving devices for experiments where samples are run on plates with identical assay configurations. The exercises on the following pages will familiarize you with the use of SDS plate documents. Getting Started 3-11
3-12 Getting Started Exercise 1: Creating a Plate Document You will need to create a plate document for every plate you run on the 7900HT instrument. The following procedure explains how to create a plate document using the SDS software. To create a plate document: Step Action 1 If not already active, launch the SDS software as explained on page 3-7. The SDS software workspace appears. 2 Choose one of the following options: ♦ Click the New Document button ( ) from the General toolbar, or ♦ From the File menu, select New. The New Document dialog appears. IMPORTANT The SDS software can handle multiple documents simultaneously, however the processing speed of your computer will decrease with each open document. For that reason, Applied Biosystems recommends limiting the number of open documents to 10. 3 Configure the New Document dialog box with the following settings: Drop-Down List Select… Assay Absolute Quantification Container 384 Wells Clear Plate Template Blank Template 4 Click OK. The software displays a new plate document with appropriate attributes. Exercise 2: Saving a Plate Document The Save command stores any changes to the plate document setup information and display settings. The following procedure explains how to save the open plate document. To save the plate document: Step Action 1 Choose one of the following options: ♦ Click the Save button ( ) from the General toolbar, or ♦ From the File menu, select Save As. 2 From the File of type drop-down list, select ABI PRISM SDS Single Plate (*.sds). 3 Click the File name text field, and type Practice. 4 Click Save. The software saves the plate document to a file entitled Practice.sds. Note Do not close the plate document at this time.
Page 1 and 2: ABI PRISM ® 7900HT Sequence Detect
Page 3 and 4: © Copyright 2001, Applied Biosyste
Page 5 and 6: iv Section:PlateDocumentSetup......
Page 7 and 8: vi A Theory of Operation Fluorescen
Page 9 and 10: Attention Words and Warning Labels
Page 11 and 12: About Waste Profiles A waste profil
Page 13 and 14: Safe Instrument Use Before Operatin
Page 16 and 17: Product Overview 2 In This Chapter
Page 18 and 19: Section: Getting to Know the Hardwa
Page 20 and 21: Interchangeable Thermal Cycler Bloc
Page 22 and 23: Computer Description The computer c
Page 24 and 25: Zymark Twister Microplate Handler D
Page 26 and 27: Instrument Connections Electrical C
Page 28 and 29: Section: Getting to Know the Softwa
Page 30 and 31: Managing Sequence Detection System
Page 32 and 33: Getting Started 3 In This Chapter T
Page 34 and 35: Using the SDS Software Online Help
Page 36 and 37: Turning on the ABI PRISM 7900HT Seq
Page 38 and 39: Using the SDS Software Workspace La
Page 40 and 41: Using the General Toolbar Using the
Page 44 and 45: Exercise 3: Opening a Plate Documen
Page 46 and 47: Lesson 2: Viewing and Resizing Pane
Page 48 and 49: Exercise 2: Selecting Multiple Well
Page 50 and 51: Lesson 4: Using the Hand-Held Bar C
Page 52 and 53: Using SDS Plate Documents Using Mul
Page 54 and 55: Run Setup and Basic Operation 4 In
Page 56 and 57: Setup Checklists Experiments/Runs P
Page 58 and 59: Section: Plate Document Setup In Th
Page 60 and 61: Step 2 - Applying Detectors and Mar
Page 62 and 63: Creating an Allelic Discrimination
Page 64 and 65: Step 3 - Configuring the Plate Docu
Page 66 and 67: Step 4 - Programming the Plate Docu
Page 68 and 69: To create a method for the absolute
Page 70 and 71: Step 5 - Saving the Plate Document
Page 72 and 73: Step 7 - Applying Sample and Plate
Page 74 and 75: Section: Running an Individual Plat
Page 76 and 77: Preparing and Running a Single Plat
Page 78 and 79: Operating the 7900HT Instrument Usi
Page 80 and 81: After the Run Analyzing the Run Dat
Page 82 and 83: Section: Running Multiple Plates Us
Page 84 and 85: Adding a Plate Document to the Plat
Page 86 and 87: To create plate documents from a te
Page 88 and 89: Adding Plates to the Plate Queue Re
Page 90 and 91: Loading Plates To load plates onto
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End-Point Analysis 5 In This Chapte
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Section: Allelic Discrimination In
Page 96 and 97:
Algorithmic Manipulation of Raw All
Page 98 and 99:
Before You Begin Using SDS Online H
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Analyzing a Completed Allelic Discr
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Calling Allele Types To call allele
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Scrutinizing the Allele Calls To an
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After the Analysis Changing the Pla
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Real-Time Runs on the 7900HT Instru
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Overview About Absolute Quantificat
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Before You Begin Using SDS Online H
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Analyzing the Run Data Configuring
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Setting the Baseline and Threshold
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Eliminating Outliers For any PCR, e
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Viewing the Standard Curve 6-14 Rea
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6-16 Real-Time Analysis
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Overview About Dissociation Curve A
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Analysis Checklist WhereYouArein th
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Determining T m Values for the Anal
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After the Analysis Changing the Pla
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Recommended Maintenance Schedule Ma
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Replacing the Sample Block When to
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7-6 System Maintenance To remove th
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7-8 System Maintenance To replace t
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7-10 System Maintenance To replace
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Cleaning the Sample Block Wells 7-1
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Prepare a Background Plate Document
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Extracting the Background 7-16 Syst
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Materials Required The following ma
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Extracting Pure Dye Information fro
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Constructing a Custom Pure Dye Plat
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Verifying Instrument Performance Us
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Preparing and Running an RNase P Pl
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Adjusting the Sensitivity of the Pl
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Testing the Adjustment 7-30 System
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Aligning the Plate Handler When to
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7-34 System Maintenance To align th
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Re-checking the Input Stack 1 7-36
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Defining the Positions of the Remai
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Aligning the Fixed-Position Bar Cod
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7-42 System Maintenance To position
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7-44 System Maintenance
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General Computer Maintenance Mainte
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Maintaining the SDS software Admini
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Troubleshooting Table 8-2 Troublesh
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Low Precision or Irreproducibility
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Writing on the Reaction Plates Fluo
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Background Runs Background Troubles
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Pure Dye Runs Pure Dye Troubleshoot
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8-12 Troubleshooting Troubleshootin
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Software and 7900HT Instrument Trou
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8-16 Troubleshooting Troubleshootin
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User Bulletins 9 9 About This Chapt
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Fluorescent-Based Chemistries Funda
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Fluorescence Detection and Data Col
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Normalization of Reporter Signals A
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Determining Initial Template Concen
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Calculating Threshold Cycles A-10 T
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Importing and Exporting Plate Docum
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Configuring the Setup Table File wi
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About the Setup Table File Format S
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Setup Table Elements (continued) Nu
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Exporting Plate Document Data Expor
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Designing TaqMan Assays C In This A
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Design Probes and Primers The follo
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Design Tips for Allelic Discriminat
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Kits, Reagents and Consumables D In
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Consumables and Disposables The ABI
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TaqMan Pre-Developed Assays and Rea
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Contacting Technical Support F Serv
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G-2 Limited Warranty Statement No a
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A(continued) Automation Controller
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I(continued) installing plate adapt
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Q quantifying probes and primers C-
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Headquarters 850 Lincoln Centre Dri
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